SMTL ID : 7f3z.1

Double mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS-K1, C59R+S108N) complexed with Trimethoprim (TOP), NADPH and dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 28 residues within 4Å: Chain A: C.15, A.16, L.40, G.41, G.44, V.45, L.46, W.48, G.105, R.106, T.107, N.108, S.111, L.127, S.128, R.129, T.130, N.144, I.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: TOP.3 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.40, A:Y.170 Hydrogen bonds: A:A.16, A:L.40, A:G.44, A:G.105, A:R.106, A:T.107, A:T.107, A:N.108, A:S.111, A:S.111, A:R.129, A:R.129, A:R.129, A:T.130, A:T.130, A:G.165, A:G.166, A:S.167, A:V.168, A:V.169, A:Y.170, A:E.172 Water bridges: A:V.146 Salt bridges: A:R.106 pi-Cation interactions: A:R.129 NDP.5: 29 residues within 4Å: Chain B: C.15, A.16, L.40, G.41, G.44, V.45, L.46, W.48, G.105, R.106, T.107, N.108, S.111, L.127, S.128, R.129, T.130, N.144, K.145, V.146, I.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172 Ligands: TOP.7 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.40 Hydrogen bonds: B:A.16, B:L.40, B:G.44, B:V.45, B:G.105, B:G.105, B:R.106, B:T.107, B:T.107, B:N.108, B:S.111, B:R.129, B:T.130, B:T.130, B:G.166, B:S.167, B:V.168, B:V.169, B:E.172 Salt bridges: B:R.106 pi-Cation interactions: B:R.129

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.2: 13 residues within 4Å: Chain A: L.487, C.490, H.491, Q.509, R.510, S.511, D.513, G.517, N.521, H.551, Y.553 Chain B: R.470, R.471 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.509, A:S.511, A:S.511, A:D.513, A:N.521, A:N.521, A:H.551, A:Y.553 Salt bridges: A:R.510, B:R.470, B:R.471 UMP.6: 15 residues within 4Å: Chain A: R.470, R.471 Chain B: R.345, L.487, C.490, H.491, Q.509, R.510, S.511, C.512, D.513, G.517, N.521, H.551, Y.553 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Salt bridges: A:R.470, A:R.471, B:R.345, B:R.510 Hydrophobic interactions: B:D.513 Hydrogen bonds: B:Q.509, B:S.511, B:D.513, B:N.521, B:N.521, B:H.551

2 x TOP: TRIMETHOPRIM(Non-covalent)

TOP.3: 15 residues within 4Å: Chain A: I.14, C.15, A.16, L.46, D.54, M.55, F.58, N.108, S.111, I.112, P.113, I.164, Y.170, T.185 Ligands: NDP.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.58 Hydrogen bonds: A:I.14, A:C.15, A:T.185 Water bridges: A:C.15 Salt bridges: A:D.54 TOP.7: 14 residues within 4Å: Chain B: I.14, C.15, A.16, L.46, D.54, M.55, F.58, N.108, S.111, P.113, I.164, Y.170, T.185 Ligands: NDP.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.58 Hydrogen bonds: B:I.14, B:C.15, B:Y.170, B:T.185 Salt bridges: B:D.54 pi-Stacking: B:F.58

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: V.453, Q.455, N.458, L.462, R.471 Chain B: V.479 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.458, A:R.471 GOL.8: 6 residues within 4Å: Chain A: L.482 Chain B: V.453, Q.455, N.458, L.462, R.471 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.458, B:R.471

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanramluk, D. et al., MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances. Structure (2022)

Release Date

2021-09-22

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional dihydrofolate reductase-thymidylate synthase